PhyloXML

PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition ( XSD) language.

A shortcoming of current formats for describing phylogenetic trees (such as Nexus and Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: species names, branch lengths, and possibly multiple support values). Data storage and exchange is even more cumbersome in studies in which trees are the result of a reconciliation of some kind:

* gene-function studies (requires annotation of nodes with taxonomic information as well as gene names, and possibly gene-duplication data)
* evolution of host-parasite interactions (requires annotation of tree nodes with taxonomic information for both host and parasite)
* phylogeographic studies (requires annotation of tree nodes with taxonomic and geographic information)

To alleviate this, a variety of ad-hoc, special purpose formats have come into use (such as the NHX format, which focuses on the needs of gene-function and phylogenomic studies).

A well defined XML format addresses these problems in a general and extensible manner and allows for interoperability between specialized and general purpose software.

An example of a program for visualizing phyloXML is Archaeopteryx.

Basic phyloXML example

example from Prof. Joe Felsenstein's book "Inferring Phylogenies"
MrBayes based on MAFFT alignment


0.88

A


B



C

References

External links

www.phyloxml.orgArchaeopteryx program

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XML-based standards
Phylogenetics software
Biological_sequence_format